Sorry, should have written this as a comment but not enough rep; have you tried query substitutions?
Something like
<property name="query.substitutions">
true 1, false 0, true 'y', false 'n'
</property>
should work
Edit after comment: as keyess has pointed out, for fluent nhibernate, something like this
var props = new Dictionary<string, string>();
props.Add("query.substitutions","true=1;false=0")
props.Add("query.substitutions","true=yes;false=no")
props.Add(...)
var sessionFactory = Fluently.Configure().BuildConfiguration().AddProperties(props);
should work (see this answer)
Also, another approach may be used based on IUserType